mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 249 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 1,865,240 | 0 | G | T | 58.4% | 63.4 / 163.4 | 125 | Q133K (CAG→AAG) | yeaE | methylglyoxal reductase YeaE |
| * | NC_000913 | 1,634,404 | 0 | A | G | 56.5% | 0.6 / 59.2 | 47 | I161T (ATC→ACC) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 807,343 | 0 | C | G | 56.2% | ‑3.0 / 22.9 | 16 | intergenic (‑62/+90) | ybhC/ybhB | outer membrane lipoprotein YbhC/putative kinase inhibitor |
| * | NC_000913 | 579,134 | 0 | T | C | 53.0% | 36.3 / inf | 264 | intergenic (‑241/+50) | borD/ybcV | prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 579,127 | 0 | T | C | 52.8% | 36.7 / inf | 267 | intergenic (‑234/+57) | borD/ybcV | prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 1,634,388 | 0 | T | G | 52.6% | 5.5 / 50.6 | 38 | A166A (GCA→GCC) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,699 | 0 | A | C | 52.6% | 34.3 / 256.1 | 173 | S63A (TCA→GCA) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,724 | 0 | G | A | 52.6% | 33.3 / 225.7 | 157 | F54F (TTC→TTT) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 579,099 | 0 | A | . | 52.4% | inf / inf | 288 | intergenic (‑206/+85) | borD/ybcV | prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 1,634,676 | 0 | A | G | 52.4% | 53.4 / 308.9 | 189 | D70D (GAT→GAC) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,661 | 0 | C | G | 52.3% | 51.5 / inf | 195 | T75T (ACG→ACC) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 579,457 | 0 | A | G | 52.2% | 17.1 / inf | 341 | I46I (ATT→ATC) | ybcV | DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 1,634,597 | 0 | C | A | 51.8% | 55.5 / 300.5 | 198 | V97F (GTT→TTT) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,658 | 0 | A | G | 51.7% | 62.0 / inf | 201 | V76V (GTT→GTC) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 579,146 | 0 | A | G | 51.7% | 10.1 / inf | 269 | intergenic (‑253/+38) | borD/ybcV | prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 1,634,382 | 0 | T | C | 51.5% | 6.8 / 44.9 | 34 | K168K (AAA→AAG) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,569 | 0 | A | T | 51.4% | 58.6 / inf | 183 | F106Y (TTT→TAT) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,571 | 0 | C | T | 51.4% | 51.5 / 277.0 | 183 | E105E (GAG→GAA) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,634,578 | 0 | T | C | 51.3% | 55.2 / 285.3 | 185 | E103G (GAA→GGA) | tfaQ | putative tail fiber assembly protein TfaQ |
| * | NC_000913 | 1,636,503 | 0 | T | C | 51.3% | 34.9 / inf | 232 | intergenic (‑136/‑253) | nohA/ynfO | putative prophage DNA‑packaging protein NohA/DUF3950 domain‑containing protein YnfO |
| Marginal new junction evidence (lowest skew 10 of 22 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 3631216 | 201 (1.910) | 46 (0.440) | 36/598 | 2.0 | 18.6% | coding (1375/1623 nt) | yhiJ | DUF4049 domain‑containing protein YhiJ |
| ? | NC_000913 | 3652036 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 259128 | 89 (0.850) | 28 (0.270) | 24/598 | 3.5 | 23.9% | coding (973/1056 nt) | phoE | outer membrane porin PhoE |
| ? | NC_000913 | 574591 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 566774 | 108 (1.030) | 47 (0.450) | 18/594 | 4.7 | 29.5% | pseudogene (91/93 nt) | renD | protein RenD |
| ? | NC_000913 | 568036 = | 117 (1.120) | pseudogene (2/213 nt) | renD | protein RenD | |||||
| * | ? | NC_000913 | 1986270 = | 106 (1.020) | 21 (0.200) | 15/592 | 5.4 | 16.5% | intergenic (‑142/‑655) | araF/ftnB | arabinose ABC transporter periplasmic binding protein/putative ferritin‑like protein |
| ? | NC_000913 | 2101749 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 1392372 | 106 (1.010) | 19 (0.180) | 14/598 | 5.7 | 15.2% | coding (382/900 nt) | pgrR | DNA‑binding transcriptional repressor PgrR |
| ? | NC_000913 | = 2290113 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 696741 | 70 (0.660) | 8 (0.100) | 7/442 | 6.4 | 13.0% | intergenic (‑1/+15) | metU/glnW | tRNA‑Met/tRNA‑Gln |
| ? | NC_000913 | 697135 = | 55 (0.710) | intergenic (‑2/+378) | metT/asnB | tRNA‑Met/asparagine synthetase B | |||||
| * | ? | NC_000913 | = 4542690 | 173 (1.640) | 11 (0.110) | 10/580 | 6.8 | 6.8% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 134 (1.310) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 3648146 | 160 (1.520) | 10 (0.120) | 7/482 | 6.9 | 7.3% | intergenic (+2/‑148) | agrA/agrB | small RNA AgrA/small regulatory RNA AgrB |
| ? | NC_000913 | 3648378 = | 124 (1.460) | intergenic (+3/‑150) | agrB/arsR | small regulatory RNA AgrB/DNA‑binding transcriptional repressor ArsR | |||||
| * | ? | NC_000913 | = 2653419 | 91 (0.860) | 8 (0.080) | 8/548 | 7.2 | 9.4% | noncoding (37/100 nt) | timR | putative small regulatory RNA TimR |
| ? | NC_000913 | 2653746 = | 71 (0.740) | intergenic (‑291/‑109) | timR/ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA | |||||
| * | ? | NC_000913 | = 1286906 | 67 (0.640) | 7 (0.070) | 6/558 | 8.2 | 10.7% | coding (198/276 nt) | ychS | putative uncharacterized protein YchS |
| ? | NC_000913 | 1287557 = | 54 (0.550) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||